Variant simulator; report

Node used for reconstructing ancestral genome sequence

If a (newick) phylogenetic tree file has been provided, the visualisation of the MSA used in the calculations is shown below. The two chosen groups (i.e. ‘ingroup’ / species of interest, and outgroup) are highlighted in the tree. The outgroup, used in the computation or not, is the outgroup, which together with the reference species of interest coalesce at the node of interest, from which the ancestral sequence have been extracted. Most recent common ancestor (MRCA) is highlighted in purple and labeled. The rest of the clades in the alignment are shown in lighter grey. Regardless whether a reconstructed ancestral sequence at a node, or an outgroup, has been chosen as the ancestor, the MRCA will be highlighted.

Distribution of simulated variants across the reference genome

If an ideogram (often possible to download on the UCSC website, here) has been provided, the distribution of simulated variants is shown across the genome of the species of interest. The grey distribution corresponds to the total amount of simulated variants, whereas the red distribution corresponds to the subset that is overlapping with a corresponding non-gap ancestral sequence. If there is no forced sub-sampling due to lack of ancestral sequence, the distribution will be fully red.

Distribution of derived variants across the reference genome

If an ideogram (often possible to download on the UCSC website, here) has been provided, the distribution of derived variants is shown across the genome of the species of interest. The distribution of derived variants across the genome is shown in red.

How much of the reference genome that has an available, aligned reconstructed ancestral sequence

Table 1 Fraction of refence genome that has an available aligned reconstructed ancestral sequence. The leftmost column represents the total size of the source chromosome (in base pairs), from the species of interest. The middle column represents the size (in base pairs) of the recontructed ancestral genome (or size of aligned outgroup without gaps). The rightmost column represents the fraction of the reference genome that is covered by an ancestral sequence, i.e. the fraction of the reference with a corresponding non-gap ancestral alignment.
Size of ref. genome Size of reconstructed genome Fraction covered of ref. genome
1 274 330 532 80 611 829 0.29
2 151 935 994 38 663 251 0.25
3 132 848 913 34 945 783 0.26
4 130 910 915 35 091 582 0.27
5 104 526 007 26 834 351 0.26
6 170 843 587 47 867 152 0.28
7 121 844 099 33 714 588 0.28
8 138 966 237 37 434 940 0.27
9 139 512 083 38 643 950 0.28
10 69 359 453 16 339 902 0.24
11 79 169 978 20 009 040 0.25
12 61 602 749 16 530 035 0.27
13 208 334 590 57 962 776 0.28
14 141 755 446 36 884 151 0.26
15 140 412 725 41 640 933 0.30
16 79 944 280 24 559 472 0.31
17 63 494 081 5 666 210 0.09
18 55 982 971 16 527 503 0.30
X 125 939 595 24 847 024 0.20

Number of simulated variants

and how many are overlapping with an available ancestral sequence

Table with corresponding data:
Table 2.
Fraction of simulated SNPs that is overlapping with a reconstructed ancestral sequence. Column explanation from left to right:
i) chromosome number
ii) the total number of simulated SNPs
iii) the number of simulated SNPs that are overlapping with a non-gap align recontructed ancestral sequence.
iv) the fraction of simulated SNPs that are overlapping with a non-gap align recontructed ancestral sequence.
v) the total number of derived variants.
No of sim. SNPs Number of sim. SNPs overlapping ancestral seq. Fraction of sim. SNPs overlapping ancestral seq. Number of derived variants
1 21 049 581 6 197 104 0.29 6 523 182
2 10 922 570 2 776 068 0.25 3 168 700
3 10 716 125 2 780 458 0.26 2 963 027
4 9 861 538 2 642 938 0.27 2 864 275
5 7 697 975 1 928 296 0.25 2 197 342
6 14 204 784 3 952 557 0.28 4 010 563
7 9 473 014 2 591 167 0.27 2 735 212
8 10 702 217 2 906 715 0.27 3 163 402
9 10 928 631 3 027 617 0.28 3 223 319
10 5 497 713 1 288 943 0.23 1 454 144
11 5 950 343 1 495 689 0.25 1 666 730
12 5 208 975 1 395 306 0.27 1 383 417
13 14 870 885 4 119 824 0.28 4 628 807
14 10 378 178 2 700 388 0.26 3 017 357
15 10 815 697 3 195 461 0.30 3 351 588
16 6 672 360 2 043 644 0.31 2 033 883
17 2 489 724 216 672 0.09 471 655
18 4 992 972 1 467 009 0.29 1 417 910
X 6 418 582 1 281 998 0.20 1 848 383

Types of simulated mutations

Table with corresponding data:
Table 3
Fraction of mutation types across the simulated variants with an available corresponding ancestral sequence. Column explanation, starting from left:
i) chromosome number
ii) the total number of SNPs
iii) the fraction of transitions
iv) the fraction of transversions
v) the fraction of CpG site mutations
vi) the fraction of non-CpG mutations (transitions + transversions)
No. of SNPs Fraction transitions Fraction transversions Fraction CpGs Fraction non-CpGs (1-CpGs)
1 6 197 104 0.51 0.33 0.16 0.84
2 2 776 068 0.48 0.31 0.21 0.79
3 2 780 458 0.47 0.30 0.23 0.77
4 2 642 938 0.49 0.32 0.19 0.81
5 1 928 296 0.49 0.32 0.20 0.80
6 3 952 557 0.47 0.30 0.23 0.77
7 2 591 167 0.49 0.31 0.20 0.80
8 2 906 715 0.50 0.33 0.18 0.82
9 3 027 617 0.50 0.32 0.18 0.82
10 1 288 943 0.47 0.30 0.23 0.77
11 1 495 689 0.48 0.32 0.20 0.80
12 1 395 306 0.44 0.28 0.27 0.73
13 4 119 824 0.51 0.34 0.15 0.85
14 2 700 388 0.48 0.31 0.21 0.79
15 3 195 461 0.51 0.34 0.15 0.85
16 2 043 644 0.51 0.33 0.15 0.85
17 216 672 0.32 0.21 0.47 0.53
18 1 467 009 0.48 0.31 0.21 0.79
X 1 281 998 0.46 0.30 0.24 0.76

Types of derived mutations*

  • CpG mutation information is not available.

##### Table with corresponding data:

Table 4
Fraction of mutation types across the derived variants. Column explanation, starting from left:
i) chromosome number
ii) the total number of SNPs
iii) the fraction of transitions
iv) the fraction of transversions.
No. of SNPs Fraction transitions Fraction transversions
1 6 523 182 0.61 0.39
2 3 168 700 0.61 0.39
3 2 963 027 0.60 0.40
4 2 864 275 0.61 0.39
5 2 197 342 0.61 0.39
6 4 010 563 0.61 0.39
7 2 735 212 0.61 0.39
8 3 163 402 0.60 0.40
9 3 223 319 0.61 0.39
10 1 454 144 0.58 0.42
11 1 666 730 0.59 0.41
12 1 383 417 0.60 0.40
13 4 628 807 0.62 0.38
14 3 017 357 0.61 0.39
15 3 351 588 0.61 0.39
16 2 033 883 0.61 0.39
17 471 655 0.60 0.40
18 1 417 910 0.60 0.40
X 1 848 383 0.60 0.40

Visualisation of gene density

and CDS overlap

Validation of simulation parameters

Number of mutations, fractions, and substitution rates. To make sure the simulation was performed as expected, the leftmost part is the calculated numbers and rates in the parameter files, including the total number of simulated variants per chromosome, based on information from the ancestor and reference species. The middle part is the (re)calculated numbers and rates based on the total number of simulated variants. The rightmost part is the (re)calculated numbers and rates within the subset with a corresponding non-gap ancestral sequence. The comparison of parameters and simulated variants is to make sure that the simulation has been perform as intended, and the comparison between total set and the subset is to make sure that the distribution is the same even if the variants are forced to be down-sampled due to the lack of an available ancestral sequence.

Comparison of numebr of mutations between log files and actual simulated files
Parameter files
Simulated variant file
Simulated variant file
(filtered for positions with a corresponding non-gap ancestral position)
Chromosome considered: 1 Chromosome considered: 1 Chromosome considered: 1
Total mut: 8517711 Total mut: 17753709 Total mut: 5217985
#AC AG AT #AC AG AT #AC AG AT
617539 1413423 512332 1391838 3023044 1009484 409330 887135 296136
7.25% 16.59% 6.01% 7.84% 17.03% 5.69% 7.84% 17.00% 5.68%
#CA CG CT #CA CG CT #CA CG CT
284204 249661 1184303 557427 553348 2335376 164672 163566 689363
3.34% 2.93% 13.90% 3.14% 3.12% 13.15% 3.16% 3.13% 13.21%
#GA GC GT #GA GC GT #GA GC GT
1183741 250146 285643 2340131 555019 557495 689485 163256 164203
13.90% 2.94% 3.35% 13.18% 3.13% 3.14% 13.21% 3.13% 3.15%
#TA TC TG #TA TC TG #TA TC TG
511433 1408898 616388 1011685 3022276 1396586 296136 886393 408310
6.00% 16.54% 7.24% 5.70% 17.02% 7.87% 5.68% 16.99% 7.83%
Total CpG mut: 1101137 Total CpG mut: 3295872 Total CpG mut: 979119
#CA CG CT (CpG) #CA CG CT (CpG) #CA CG CT (CpG)
99284 86004 365221 290867 284143 1072705 86926 84095 318342
9.02% 7.81% 33.17% 8.83% 8.62% 32.55% 8.88% 8.59% 32.51%
#GA GC GT (CpG) #GA GC GT (CpG) #GA GC GT (CpG)
365004 86065 99559 1073134 284804 290219 318788 84381 86587
33.15% 7.82% 9.04% 32.56% 8.64% 8.81% 32.56% 8.62% 8.84%
Chromosome considered: 2 Chromosome considered: 2 Chromosome considered: 2
Total mut: 4162168 Total mut: 26366504 Total mut: 7413230
#AC AG AT #AC AG AT #AC AG AT
324455 701973 235396 2044410 4439741 1481866 578000 1251259 417279
7.80% 16.87% 5.66% 7.75% 16.84% 5.62% 7.80% 16.88% 5.63%
#CA CG CT #CA CG CT #CA CG CT
130685 134173 553280 840850 835858 3527871 236107 234856 988890
3.14% 3.22% 13.29% 3.19% 3.17% 13.38% 3.18% 3.17% 13.34%
#GA GC GT #GA GC GT #GA GC GT
554275 134487 130499 3533274 838346 842493 988847 234705 235664
13.32% 3.23% 3.14% 13.40% 3.18% 3.20% 13.34% 3.17% 3.18%
#TA TC TG #TA TC TG #TA TC TG
236127 702090 324728 1485979 4443961 2051855 418038 1252642 576943
5.67% 16.87% 7.80% 5.64% 16.85% 7.78% 5.64% 16.90% 7.78%
Total CpG mut: 554956 Total CpG mut: 5605647 Total CpG mut: 1559942
#CA CG CT (CpG) #CA CG CT (CpG) #CA CG CT (CpG)
48335 47911 181200 494765 483682 1825156 137972 134497 507441
8.71% 8.63% 32.65% 8.83% 8.63% 32.56% 8.84% 8.62% 32.53%
#GA GC GT (CpG) #GA GC GT (CpG) #GA GC GT (CpG)
181355 48104 48051 1823932 484365 493747 507946 134511 137575
32.68% 8.67% 8.66% 32.54% 8.64% 8.81% 32.56% 8.62% 8.82%
Chromosome considered: 3 Chromosome considered: 3 Chromosome considered: 3
Total mut: 3968978 Total mut: 34530717 Total mut: 9563063
#AC AG AT #AC AG AT #AC AG AT
337082 696480 213655 2648692 5750302 1919494 738289 1599520 533811
8.49% 17.55% 5.38% 7.67% 16.65% 5.56% 7.72% 16.73% 5.58%
#CA CG CT #CA CG CT #CA CG CT
114362 131436 492332 1120095 1112484 4697396 308599 307023 1293072
2.88% 3.31% 12.40% 3.24% 3.22% 13.60% 3.23% 3.21% 13.52%
#GA GC GT #GA GC GT #GA GC GT
490564 131204 114026 4705633 1115990 1122327 1294148 307200 308289
12.36% 3.31% 2.87% 13.63% 3.23% 3.25% 13.53% 3.21% 3.22%
#TA TC TG #TA TC TG #TA TC TG
213962 696730 337145 1924868 5756640 2656796 534676 1600756 737680
5.39% 17.55% 8.49% 5.57% 16.67% 7.69% 5.59% 16.74% 7.71%
Total CpG mut: 544278 Total CpG mut: 8157559 Total CpG mut: 2190567
#CA CG CT (CpG) #CA CG CT (CpG) #CA CG CT (CpG)
46140 52512 173904 720285 704236 2654870 193595 189215 712567
8.48% 9.65% 31.95% 8.83% 8.63% 32.54% 8.84% 8.64% 32.53%
#GA GC GT (CpG) #GA GC GT (CpG) #GA GC GT (CpG)
173903 51984 45835 2654333 705501 718334 712923 189298 192969
31.95% 9.55% 8.42% 32.54% 8.65% 8.81% 32.55% 8.64% 8.81%
Chromosome considered: 4 Chromosome considered: 4 Chromosome considered: 4
Total mut: 3832191 Total mut: 42464311 Total mut: 11690736
#AC AG AT #AC AG AT #AC AG AT
318833 683813 215942 3259153 7075786 2361844 901433 1954783 652124
8.32% 17.84% 5.63% 7.68% 16.66% 5.56% 7.71% 16.72% 5.58%
#CA CG CT #CA CG CT #CA CG CT
109297 114683 472660 1375690 1368194 5773243 376905 375479 1582087
2.85% 2.99% 12.33% 3.24% 3.22% 13.60% 3.22% 3.21% 13.53%
#GA GC GT #GA GC GT #GA GC GT
473196 115866 109776 5783237 1370934 1379441 1583563 375578 377692
12.35% 3.02% 2.86% 13.62% 3.23% 3.25% 13.55% 3.21% 3.23%
#TA TC TG #TA TC TG #TA TC TG
215703 683912 318510 2368376 7080772 3267641 653933 1956017 901142
5.63% 17.85% 8.31% 5.58% 16.67% 7.70% 5.59% 16.73% 7.71%
Total CpG mut: 437795 Total CpG mut: 10085503 Total CpG mut: 2705832
#CA CG CT (CpG) #CA CG CT (CpG) #CA CG CT (CpG)
38671 38225 141567 890912 870080 3282201 239438 233604 880113
8.83% 8.73% 32.34% 8.83% 8.63% 32.54% 8.85% 8.63% 32.53%
#GA GC GT (CpG) #GA GC GT (CpG) #GA GC GT (CpG)
142030 38574 38728 3281853 872692 887765 881047 233712 237918
32.44% 8.81% 8.85% 32.54% 8.65% 8.80% 32.56% 8.64% 8.79%
Chromosome considered: 5 Chromosome considered: 5 Chromosome considered: 5
Total mut: 2911411 Total mut: 48471012 Total mut: 13238806
#AC AG AT #AC AG AT #AC AG AT
234917 509748 166665 3716542 8068888 2694239 1021072 2215278 739442
8.07% 17.51% 5.72% 7.67% 16.65% 5.56% 7.71% 16.73% 5.59%
#CA CG CT #CA CG CT #CA CG CT
85818 85538 370882 1571693 1564104 6600198 425522 424659 1789295
2.95% 2.94% 12.74% 3.24% 3.23% 13.62% 3.21% 3.21% 13.52%
#GA GC GT #GA GC GT #GA GC GT
371363 85432 86751 6610499 1566913 1575899 1790488 424544 426848
12.76% 2.93% 2.98% 13.64% 3.23% 3.25% 13.52% 3.21% 3.22%
#TA TC TG #TA TC TG #TA TC TG
167071 511448 235778 2700481 8075347 3726209 741410 2218539 1021709
5.74% 17.57% 8.10% 5.57% 16.66% 7.69% 5.60% 16.76% 7.72%
Total CpG mut: 326558 Total CpG mut: 11776777 Total CpG mut: 3086058
#CA CG CT (CpG) #CA CG CT (CpG) #CA CG CT (CpG)
28942 27562 106755 1040064 1016296 3832471 272853 266684 1003503
8.86% 8.44% 32.69% 8.83% 8.63% 32.54% 8.84% 8.64% 32.52%
#GA GC GT (CpG) #GA GC GT (CpG) #GA GC GT (CpG)
106994 27442 28863 3832420 1018532 1036994 1005154 266454 271410
32.76% 8.40% 8.84% 32.54% 8.65% 8.81% 32.57% 8.63% 8.79%
Chromosome considered: 6 Chromosome considered: 6 Chromosome considered: 6
Total mut: 5313121 Total mut: 59381443 Total mut: 16300771
#AC AG AT #AC AG AT #AC AG AT
441499 927342 283818 4516592 9805897 3274848 1246855 2706953 903549
8.31% 17.45% 5.34% 7.61% 16.51% 5.51% 7.65% 16.61% 5.54%
#CA CG CT #CA CG CT #CA CG CT
155586 177546 671887 1949676 1939592 8184434 530691 529328 2231662
2.93% 3.34% 12.65% 3.28% 3.27% 13.78% 3.26% 3.25% 13.69%
#GA GC GT #GA GC GT #GA GC GT
671004 177634 154936 8193971 1942793 1953217 2231058 529581 531304
12.63% 3.34% 2.92% 13.80% 3.27% 3.29% 13.69% 3.25% 3.26%
#TA TC TG #TA TC TG #TA TC TG
284456 927104 440309 3281363 9811226 4527834 905252 2706777 1247761
5.35% 17.45% 8.29% 5.53% 16.52% 7.62% 5.55% 16.61% 7.65%
Total CpG mut: 752069 Total CpG mut: 15071130 Total CpG mut: 3976650
#CA CG CT (CpG) #CA CG CT (CpG) #CA CG CT (CpG)
63124 70380 242622 1330610 1300005 4905822 351282 343329 1293629
8.39% 9.36% 32.26% 8.83% 8.63% 32.55% 8.83% 8.63% 32.53%
#GA GC GT (CpG) #GA GC GT (CpG) #GA GC GT (CpG)
242092 70987 62864 4904134 1303120 1327439 1295005 343328 350077
32.19% 9.44% 8.36% 32.54% 8.65% 8.81% 32.57% 8.63% 8.80%
Chromosome considered: 7 Chromosome considered: 7 Chromosome considered: 7
Total mut: 3619980 Total mut: 66858569 Total mut: 18372922
#AC AG AT #AC AG AT #AC AG AT
294871 628222 201470 5078781 11027110 3681558 1403640 3046744 1017073
8.15% 17.35% 5.57% 7.60% 16.49% 5.51% 7.64% 16.58% 5.54%
#CA CG CT #CA CG CT #CA CG CT
106266 112621 468053 2200653 2187781 9233621 599429 597428 2519966
2.94% 3.11% 12.93% 3.29% 3.27% 13.81% 3.26% 3.25% 13.72%
#GA GC GT #GA GC GT #GA GC GT
468815 112833 106391 9245638 2191271 2203117 2520436 597982 600205
12.95% 3.12% 2.94% 13.83% 3.28% 3.30% 13.72% 3.25% 3.27%
#TA TC TG #TA TC TG #TA TC TG
202027 622822 295589 3688239 11031151 5089649 1019039 3046623 1404357
5.58% 17.21% 8.17% 5.52% 16.50% 7.61% 5.55% 16.58% 7.64%
Total CpG mut: 474644 Total CpG mut: 17067018 Total CpG mut: 4495666
#CA CG CT (CpG) #CA CG CT (CpG) #CA CG CT (CpG)
40120 41425 155459 1506779 1471208 5555969 396872 387304 1463266
8.45% 8.73% 32.75% 8.83% 8.62% 32.55% 8.83% 8.62% 32.55%
#GA GC GT (CpG) #GA GC GT (CpG) #GA GC GT (CpG)
155659 41508 40473 5554998 1474593 1503471 1464470 388004 395750
32.79% 8.75% 8.53% 32.55% 8.64% 8.81% 32.58% 8.63% 8.80%
Chromosome considered: 8 Chromosome considered: 8 Chromosome considered: 8
Total mut: 4264059 Total mut: 75720475 Total mut: 20758104
#AC AG AT #AC AG AT #AC AG AT
344802 751529 255938 5780648 12551526 4189068 1592308 3454627 1152871
8.09% 17.62% 6.00% 7.63% 16.58% 5.53% 7.67% 16.64% 5.55%
#CA CG CT #CA CG CT #CA CG CT
129517 122736 527016 2473640 2460520 10382768 673287 670989 2831781
3.04% 2.88% 12.36% 3.27% 3.25% 13.71% 3.24% 3.23% 13.64%
#GA GC GT #GA GC GT #GA GC GT
528085 122830 130268 10391327 2463884 2476245 2830721 671933 674229
12.38% 2.88% 3.06% 13.72% 3.25% 3.27% 13.64% 3.24% 3.25%
#TA TC TG #TA TC TG #TA TC TG
256172 751191 343975 4198286 12557814 5794749 1156013 3455713 1593632
6.01% 17.62% 8.07% 5.54% 16.58% 7.65% 5.57% 16.65% 7.68%
Total CpG mut: 452232 Total CpG mut: 18907329 Total CpG mut: 5017199
#CA CG CT (CpG) #CA CG CT (CpG) #CA CG CT (CpG)
42023 38417 145372 1669342 1629559 6155307 442777 432402 1632860
9.29% 8.49% 32.15% 8.83% 8.62% 32.56% 8.83% 8.62% 32.55%
#GA GC GT (CpG) #GA GC GT (CpG) #GA GC GT (CpG)
145436 38831 42153 6154315 1633180 1665626 1634555 432875 441730
32.16% 8.59% 9.32% 32.55% 8.64% 8.81% 32.58% 8.63% 8.80%
Chromosome considered: 9 Chromosome considered: 9 Chromosome considered: 9
Total mut: 4307566 Total mut: 84658165 Total mut: 23234053
#AC AG AT #AC AG AT #AC AG AT
345838 751358 247064 6470084 14047680 4687565 1783208 3869317 1290224
8.03% 17.44% 5.74% 7.64% 16.59% 5.54% 7.67% 16.65% 5.55%
#CA CG CT #CA CG CT #CA CG CT
127508 131353 548573 2760438 2747059 11585563 753289 750544 3166134
2.96% 3.05% 12.74% 3.26% 3.24% 13.69% 3.24% 3.23% 13.63%
#GA GC GT #GA GC GT #GA GC GT
551480 132299 129495 11600099 2749882 2764057 3166080 751073 754026
12.80% 3.07% 3.01% 13.70% 3.25% 3.26% 13.63% 3.23% 3.25%
#TA TC TG #TA TC TG #TA TC TG
246227 748419 347952 4699413 14058695 6487630 1293974 3871095 1785089
5.72% 17.37% 8.08% 5.55% 16.61% 7.66% 5.57% 16.66% 7.68%
Total CpG mut: 503825 Total CpG mut: 20898270 Total CpG mut: 5568867
#CA CG CT (CpG) #CA CG CT (CpG) #CA CG CT (CpG)
44544 43280 164451 1844816 1801206 6803783 491296 479927 1812520
8.84% 8.59% 32.64% 8.83% 8.62% 32.56% 8.82% 8.62% 32.55%
#GA GC GT (CpG) #GA GC GT (CpG) #GA GC GT (CpG)
164628 42712 44210 6801910 1805743 1840812 1813962 481044 490118
32.68% 8.48% 8.77% 32.55% 8.64% 8.81% 32.57% 8.64% 8.80%
Chromosome considered: 10 Chromosome considered: 10 Chromosome considered: 10
Total mut: 2040392 Total mut: 88860175 Total mut: 24227250
#AC AG AT #AC AG AT #AC AG AT
200476 383881 110501 6787959 14739410 4918641 1858630 4033141 1345020
9.83% 18.81% 5.42% 7.64% 16.59% 5.54% 7.67% 16.65% 5.55%
#CA CG CT #CA CG CT #CA CG CT
50420 64686 212135 2899839 2884325 12167796 785893 782548 3302679
2.47% 3.17% 10.40% 3.26% 3.25% 13.69% 3.24% 3.23% 13.63%
#GA GC GT #GA GC GT #GA GC GT
211316 63861 50078 12182052 2887662 2903044 3303092 783464 786816
10.36% 3.13% 2.45% 13.71% 3.25% 3.27% 13.63% 3.23% 3.25%
#TA TC TG #TA TC TG #TA TC TG
111274 381888 199876 4930174 14751902 6807371 1348712 4036020 1861235
5.45% 18.72% 9.80% 5.55% 16.60% 7.66% 5.57% 16.66% 7.68%
Total CpG mut: 217225 Total CpG mut: 22193973 Total CpG mut: 5864613
#CA CG CT (CpG) #CA CG CT (CpG) #CA CG CT (CpG)
18591 22319 68081 1958857 1912764 7225596 517120 505492 1908783
8.56% 10.27% 31.34% 8.83% 8.62% 32.56% 8.82% 8.62% 32.55%
#GA GC GT (CpG) #GA GC GT (CpG) #GA GC GT (CpG)
67346 22396 18492 7224645 1917142 1954969 1910762 506435 516021
31.00% 10.31% 8.51% 32.55% 8.64% 8.81% 32.58% 8.64% 8.80%
Chromosome considered: 11 Chromosome considered: 11 Chromosome considered: 11
Total mut: 2283812 Total mut: 93581940 Total mut: 25422266
#AC AG AT #AC AG AT #AC AG AT
199243 414996 134339 7156995 15542098 5186577 1952315 4236473 1413225
8.72% 18.17% 5.88% 7.65% 16.61% 5.54% 7.68% 16.66% 5.56%
#CA CG CT #CA CG CT #CA CG CT
65026 67109 258421 3047993 3031829 12788353 823038 820086 3459289
2.85% 2.94% 11.32% 3.26% 3.24% 13.67% 3.24% 3.23% 13.61%
#GA GC GT #GA GC GT #GA GC GT
256990 67304 64496 12802847 3035511 3050420 3460260 820794 823971
11.25% 2.95% 2.82% 13.68% 3.24% 3.26% 13.61% 3.23% 3.24%
#TA TC TG #TA TC TG #TA TC TG
135640 419606 200642 5200890 15558677 7179750 1417255 4240061 1955499
5.94% 18.37% 8.79% 5.56% 16.63% 7.67% 5.57% 16.68% 7.69%
Total CpG mut: 230040 Total CpG mut: 23422551 Total CpG mut: 6165286
#CA CG CT (CpG) #CA CG CT (CpG) #CA CG CT (CpG)
21289 21517 72274 2067551 2018794 7625428 543668 531456 2006477
9.25% 9.35% 31.42% 8.83% 8.62% 32.56% 8.82% 8.62% 32.54%
#GA GC GT (CpG) #GA GC GT (CpG) #GA GC GT (CpG)
72252 21597 21111 7625016 2023005 2062757 2008610 532538 542537
31.41% 9.39% 9.18% 32.55% 8.64% 8.81% 32.58% 8.64% 8.80%
Chromosome considered: 12 Chromosome considered: 12 Chromosome considered: 12
Total mut: 1856006 Total mut: 97349502 Total mut: 26435404
#AC AG AT #AC AG AT #AC AG AT
173145 346363 90612 7421290 16116862 5377694 2023129 4390196 1464386
9.33% 18.66% 4.88% 7.62% 16.56% 5.52% 7.65% 16.61% 5.54%
#CA CG CT #CA CG CT #CA CG CT
46047 66679 207435 3185369 3168452 13364610 860105 856855 3614270
2.48% 3.59% 11.18% 3.27% 3.25% 13.73% 3.25% 3.24% 13.67%
#GA GC GT #GA GC GT #GA GC GT
207851 67312 46666 13381112 3172507 3187871 3616446 857665 860814
11.20% 3.63% 2.51% 13.75% 3.26% 3.27% 13.68% 3.24% 3.26%
#TA TC TG #TA TC TG #TA TC TG
89397 341946 172553 5393890 16134251 7445594 1469133 4395590 2026815
4.82% 18.42% 9.30% 5.54% 16.57% 7.65% 5.56% 16.63% 7.67%
Total CpG mut: 266141 Total CpG mut: 24863964 Total CpG mut: 6547454
#CA CG CT (CpG) #CA CG CT (CpG) #CA CG CT (CpG)
21236 28644 83002 2194478 2143416 8094869 577395 564470 2130753
7.98% 10.76% 31.19% 8.83% 8.62% 32.56% 8.82% 8.62% 32.54%
#GA GC GT (CpG) #GA GC GT (CpG) #GA GC GT (CpG)
82918 29115 21226 8094570 2147297 2189334 2133523 565176 576137
31.16% 10.94% 7.98% 32.56% 8.64% 8.81% 32.59% 8.63% 8.80%
Chromosome considered: 13 Chromosome considered: 13 Chromosome considered: 13
Total mut: 6022680 Total mut: 109920053 Total mut: 29931992
#AC AG AT #AC AG AT #AC AG AT
404825 963121 372206 8408671 18257895 6093100 2298153 4985144 1663760
6.72% 15.99% 6.18% 7.65% 16.61% 5.54% 7.68% 16.65% 5.56%
#CA CG CT #CA CG CT #CA CG CT
216686 174526 881047 3579220 3558574 15011574 968964 965579 4071336
3.60% 2.90% 14.63% 3.26% 3.24% 13.66% 3.24% 3.23% 13.60%
#GA GC GT #GA GC GT #GA GC GT
881898 174964 216875 15026698 3562518 3580747 4073262 966596 969669
14.64% 2.91% 3.60% 13.67% 3.24% 3.26% 13.61% 3.23% 3.24%
#TA TC TG #TA TC TG #TA TC TG
372310 959273 404949 6113728 18286926 8440402 1669797 4995503 2304229
6.18% 15.93% 6.72% 5.56% 16.64% 7.68% 5.58% 16.69% 7.70%
Total CpG mut: 791778 Total CpG mut: 27164298 Total CpG mut: 7170690
#CA CG CT (CpG) #CA CG CT (CpG) #CA CG CT (CpG)
73302 58257 263998 2397470 2341150 8844215 632396 618004 2333651
9.26% 7.36% 33.34% 8.83% 8.62% 32.56% 8.82% 8.62% 32.54%
#GA GC GT (CpG) #GA GC GT (CpG) #GA GC GT (CpG)
265061 58327 72833 8843695 2345656 2392112 2336704 618839 631096
33.48% 7.37% 9.20% 32.56% 8.64% 8.81% 32.59% 8.63% 8.80%
Chromosome considered: 14 Chromosome considered: 14 Chromosome considered: 14
Total mut: 3940231 Total mut: 118091543 Total mut: 32057108
#AC AG AT #AC AG AT #AC AG AT
307995 668170 219996 9019315 19584505 6536373 2457074 5330620 1779452
7.82% 16.96% 5.58% 7.64% 16.58% 5.54% 7.66% 16.63% 5.55%
#CA CG CT #CA CG CT #CA CG CT
122564 125001 526377 3853893 3831934 16164734 1039972 1037066 4371140
3.11% 3.17% 13.36% 3.26% 3.24% 13.69% 3.24% 3.24% 13.64%
#GA GC GT #GA GC GT #GA GC GT
528005 125066 122024 16182427 3836589 3854752 4372661 1037830 1040764
13.40% 3.17% 3.10% 13.70% 3.25% 3.26% 13.64% 3.24% 3.25%
#TA TC TG #TA TC TG #TA TC TG
220686 665483 308864 6557902 19616525 9052594 1785412 5341428 2463689
5.60% 16.89% 7.84% 5.55% 16.61% 7.67% 5.57% 16.66% 7.69%
Total CpG mut: 590985 Total CpG mut: 29370986 Total CpG mut: 7745962
#CA CG CT (CpG) #CA CG CT (CpG) #CA CG CT (CpG)
49860 51164 194375 2591872 2530630 9562967 682905 667235 2521285
8.44% 8.66% 32.89% 8.82% 8.62% 32.56% 8.82% 8.61% 32.55%
#GA GC GT (CpG) #GA GC GT (CpG) #GA GC GT (CpG)
194434 50754 50398 9561880 2537093 2586544 2523541 668992 682004
32.90% 8.59% 8.53% 32.56% 8.64% 8.81% 32.58% 8.64% 8.80%
Chromosome considered: 15 Chromosome considered: 15 Chromosome considered: 15
Total mut: 4390246 Total mut: 127243154 Total mut: 34770946
#AC AG AT #AC AG AT #AC AG AT
315132 729410 272127 9740339 21150254 7057535 2672129 5797259 1934749
7.18% 16.61% 6.20% 7.65% 16.62% 5.55% 7.68% 16.67% 5.56%
#CA CG CT #CA CG CT #CA CG CT
149545 125348 602532 4137738 4114843 17358530 1123568 1120191 4722063
3.41% 2.86% 13.72% 3.25% 3.23% 13.64% 3.23% 3.22% 13.58%
#GA GC GT #GA GC GT #GA GC GT
603760 124955 148321 17378705 4120300 4139105 4725914 1121651 1124214
13.75% 2.85% 3.38% 13.66% 3.24% 3.25% 13.59% 3.23% 3.23%
#TA TC TG #TA TC TG #TA TC TG
270847 731501 316768 7082594 21187071 9776140 1941622 5808821 2678765
6.17% 16.66% 7.22% 5.57% 16.65% 7.68% 5.58% 16.71% 7.70%
Total CpG mut: 538599 Total CpG mut: 31035072 Total CpG mut: 8227585
#CA CG CT (CpG) #CA CG CT (CpG) #CA CG CT (CpG)
50434 42472 176510 2738897 2674614 10103550 725492 708954 2677635
9.36% 7.89% 32.77% 8.83% 8.62% 32.56% 8.82% 8.62% 32.54%
#GA GC GT (CpG) #GA GC GT (CpG) #GA GC GT (CpG)
176147 42838 50198 10103895 2680804 2733312 2680420 710814 724270
32.70% 7.95% 9.32% 32.56% 8.64% 8.81% 32.58% 8.64% 8.80%
Chromosome considered: 16 Chromosome considered: 16 Chromosome considered: 16
Total mut: 2704483 Total mut: 132870149 Total mut: 36498699
#AC AG AT #AC AG AT #AC AG AT
205511 449254 160486 10184917 22111870 7378621 2808211 6092700 2033372
7.60% 16.61% 5.93% 7.67% 16.64% 5.55% 7.69% 16.69% 5.57%
#CA CG CT #CA CG CT #CA CG CT
88061 80610 361167 4314793 4290663 18100387 1178146 1174447 4951041
3.26% 2.98% 13.35% 3.25% 3.23% 13.62% 3.23% 3.22% 13.56%
#GA GC GT #GA GC GT #GA GC GT
362311 81136 86728 18119789 4295639 4314974 4953657 1175768 1178302
13.40% 3.00% 3.21% 13.64% 3.23% 3.25% 13.57% 3.22% 3.23%
#TA TC TG #TA TC TG #TA TC TG
162580 459777 206862 7401529 22140691 10216276 2039380 6100442 2813233
6.01% 17.00% 7.65% 5.57% 16.66% 7.69% 5.59% 16.71% 7.71%
Total CpG mut: 327932 Total CpG mut: 32080437 Total CpG mut: 8543476
#CA CG CT (CpG) #CA CG CT (CpG) #CA CG CT (CpG)
30079 26564 107802 2831324 2764464 10443808 753533 736023 2780325
9.17% 8.10% 32.87% 8.83% 8.62% 32.56% 8.82% 8.62% 32.54%
#GA GC GT (CpG) #GA GC GT (CpG) #GA GC GT (CpG)
107324 26852 29311 10444602 2770925 2825314 2783743 737842 752010
32.73% 8.19% 8.94% 32.56% 8.64% 8.81% 32.58% 8.64% 8.80%
Chromosome considered: 17 Chromosome considered: 17 Chromosome considered: 17
Total mut: 626875 Total mut: 134156818 Total mut: 36614219
#AC AG AT #AC AG AT #AC AG AT
50800 109863 35844 10279167 22316514 7446703 2816837 6111648 2039573
8.10% 17.53% 5.72% 7.66% 16.63% 5.55% 7.69% 16.69% 5.57%
#CA CG CT #CA CG CT #CA CG CT
19302 20663 77334 4359214 4334745 18287100 1182098 1178249 4967523
3.08% 3.30% 12.34% 3.25% 3.23% 13.63% 3.23% 3.22% 13.57%
#GA GC GT #GA GC GT #GA GC GT
76556 20687 18939 18307730 4339797 4359299 4970001 1179653 1182209
12.21% 3.30% 3.02% 13.65% 3.23% 3.25% 13.57% 3.22% 3.23%
#TA TC TG #TA TC TG #TA TC TG
35999 110274 50614 7470082 22345394 10311073 2045651 6118962 2821815
5.74% 17.59% 8.07% 5.57% 16.66% 7.69% 5.59% 16.71% 7.71%
Total CpG mut: 88873 Total CpG mut: 33283492 Total CpG mut: 8644628
#CA CG CT (CpG) #CA CG CT (CpG) #CA CG CT (CpG)
7802 8894 27965 2937727 2868154 10835389 762378 744792 2813241
8.78% 10.01% 31.47% 8.83% 8.62% 32.55% 8.82% 8.62% 32.54%
#GA GC GT (CpG) #GA GC GT (CpG) #GA GC GT (CpG)
27790 8636 7786 10835673 2875282 2931267 2816280 746899 761038
31.27% 9.72% 8.76% 32.56% 8.64% 8.81% 32.58% 8.64% 8.80%
Chromosome considered: 18 Chromosome considered: 18 Chromosome considered: 18
Total mut: 1914178 Total mut: 138097106 Total mut: 37778892
#AC AG AT #AC AG AT #AC AG AT
170495 353845 100524 10576276 22963417 7661943 2904740 6303311 2103330
8.91% 18.49% 5.25% 7.66% 16.63% 5.55% 7.69% 16.68% 5.57%
#CA CG CT #CA CG CT #CA CG CT
50073 60149 219412 4490212 4465388 18837800 1220843 1216804 5129428
2.62% 3.14% 11.46% 3.25% 3.23% 13.64% 3.23% 3.22% 13.58%
#GA GC GT #GA GC GT #GA GC GT
220754 60088 49305 18858432 4470193 4490384 5132232 1218213 1220903
11.53% 3.14% 2.58% 13.66% 3.24% 3.25% 13.58% 3.22% 3.23%
#TA TC TG #TA TC TG #TA TC TG
101339 358086 170108 7685220 22989451 10608390 2109548 6309875 2909665
5.29% 18.71% 8.89% 5.57% 16.65% 7.68% 5.58% 16.70% 7.70%
Total CpG mut: 221904 Total CpG mut: 34336176 Total CpG mut: 8946964
#CA CG CT (CpG) #CA CG CT (CpG) #CA CG CT (CpG)
18621 21665 70523 3030765 2959285 11178154 789343 771010 2911519
8.39% 9.76% 31.78% 8.83% 8.62% 32.56% 8.82% 8.62% 32.54%
#GA GC GT (CpG) #GA GC GT (CpG) #GA GC GT (CpG)
70726 21678 18691 11177818 2966286 3023868 2914316 772994 787782
31.87% 9.77% 8.42% 32.55% 8.64% 8.81% 32.57% 8.64% 8.81%
Chromosome considered: X Chromosome considered: X Chromosome considered: X
Total mut: 2391815 Total mut: 143058216 Total mut: 38756417
#AC AG AT #AC AG AT #AC AG AT
186393 402428 136808 10964826 23807671 7943740 2980874 6468624 2158726
7.79% 16.83% 5.72% 7.66% 16.64% 5.55% 7.69% 16.69% 5.57%
#CA CG CT #CA CG CT #CA CG CT
82734 74591 312614 4646074 4619796 19492132 1251533 1247203 5258865
3.46% 3.12% 13.07% 3.25% 3.23% 13.63% 3.23% 3.22% 13.57%
#GA GC GT #GA GC GT #GA GC GT
314421 74234 81941 19512673 4625104 4645822 5262373 1249188 1251704
13.15% 3.10% 3.43% 13.64% 3.23% 3.25% 13.58% 3.22% 3.23%
#TA TC TG #TA TC TG #TA TC TG
137948 400352 187351 7967929 23834650 10997799 2164914 6476095 2986318
5.77% 16.74% 7.83% 5.57% 16.66% 7.69% 5.59% 16.71% 7.71%
Total CpG mut: 271861 Total CpG mut: 35793648 Total CpG mut: 9251437
#CA CG CT (CpG) #CA CG CT (CpG) #CA CG CT (CpG)
25187 22089 88836 3159068 3084813 11652668 816296 797065 3010571
9.26% 8.13% 32.68% 8.83% 8.62% 32.56% 8.82% 8.62% 32.54%
#GA GC GT (CpG) #GA GC GT (CpG) #GA GC GT (CpG)
88744 22049 24956 11652835 3092004 3152260 3013705 799297 814503
32.64% 8.11% 9.18% 32.56% 8.64% 8.81% 32.58% 8.64% 8.80%